Getting the Eb, Bb, & C versions to connect with the index means they have to have the same offset. Even if you use just one transposition, you need to get the index matched to your copy. And it's easy to drop or duplicate a page when scanning, and pdfs acquired from questionable sources can be a mess. Missing pages wreak havoc with indexing.

The key to a long and prosperous life with iGigBook is to make sure your pdfs are cleaned up to have the exact correct number of pages. There are many PDF editors that are cheap or free, so get one and give your files a nice massage. This can be a bit tedious, but like playing long tones, it pays off.

It is massively easier to do this if the page number written on the page equals the PDF page number — that is, if page marked "10" is the 10th page of the PDF. That way you can quickly page through and spot any irregularities. Start at the end to see if the last page is right: if the last page is # 512 it should be the 512th page. Scroll forward until you find where missing pages should be.

Insert blank pages to replace any that are missing or obtain the missing pages somehow.

This is so much easier than keeping an offset in mind: it's confusing to try to remember that for this book the 10th page is marked "8" while for another book the 10th page is marked "13", etc.